I had this exact problem with the first R-09 I got from Sound Pros.
Unfortunately, I didn't get a chance to test out my R-09 until after it had already been over 30 days (due to getting repeatedly bad 2GB SD cards from an ebay seller, and the fact that no SD card came with the original R-09, I had no reason to plug mics into it if I couldn't even test out the recorder at home). So, at my first outting with it, the very first time I plugged my battery box into the R-09, the Line Input jack broke completely. It was picking up a signal (or so it appeared), but it was obviously not very usable in that condition.
Again, since I was over the 30-day warranty thing from the dealer (it was technically like 36 days), I had to go through Roland, and it was a nightmare from start to finish. (Which has made me contemplate never getting Roland products again... it should not be such a hassle to get a product that's still under warranty to be repaired/replaced). They did, however, end up sending me a new unit after a ton of time spent on the phone arguing with them. I tried the input jacks on the replacement unit, and it seems to be much better.
FWIW, the original R-09 that I got had firmware version 1.02, and as I said, it did not even come with the crappy 64 MB SD card. However, the replacement R-09 had firmware version 1.03 and came with a crappy 64 MB SD card. The newer R-09 also had specific instructions (with pictures) warning the user to use "CAUTION" when opening the (shoddy designed) battery door.
Overall, I do like the R-09 but I have to admit that I am concerned that the next time I plug mics into it, the Input jack will break. This should not be the case... I mean, come on, you can get a crappy walkman at WalMart and its input jack can take normal usage with flying colors... yet the $399 recorder by Roland flunked out on the first time when plugging something into its jack.